[BioC] dye swap vs. control channel

[Isaac Mehl]

this design brings up a question i always have.  is it "better" to do
all experiments in one channel (Cy5) and compare every sample to a
standard (cy3)?  this way you can use less arrays or do more biological
replicates.  IMHO getting repeated measurements of biological variation
is more important than dye swap.

very interested to hear what people think about this topic since it is
integral to experimental design.

-isaac



DIF1,2 and 3 are different but similar drugs...............
>>
>> Slides 1-6 are treatment 1 (DIF1) Vs No treatment
>> Slide1 Cy5/Cy3 (DIF1/no treatment)
>> Slide2 Cy3/Cy5 (DIF1/no treatment)
>> Slide3 Cy5/Cy3 (DIF1/no treatment)
>> Slide4 Cy3/Cy5 (DIF1/no treatment)
>> Slide5 Cy3/Cy5 (DIF1/no treatment)
>> Slide6 Cy5/Cy3 (DIF1/no treatment)
>>
>> Slides 7-12 are treatment 2 (DIF2) Vs No treatment
>> Slide7 Cy5/Cy3 (DIF2/no treatment)
>> Slide8 Cy3/Cy5 (DIF2/no treatment)
>> Slide9 Cy5/Cy3 (DIF2/no treatment)
>> Slide10 Cy3/Cy5 (DIF2/no treatment)
>> Slide11 Cy3/Cy5 (DIF2/no treatment)
>> Slide12 Cy5/Cy3 (DIF2/no treatment)
>>
>> Slides 13-18 are treatment 3(DIF3) Vs No treatment
>> Slide13 Cy5/Cy3 (DIF3/no treatment)
>> Slide14 Cy3/Cy5 (DIF3/no treatment)
>> Slide15 Cy5/Cy3 (DIF3/no treatment)
>> Slide16 Cy3/Cy5 (DIF3/no treatment)
>> Slide17 Cy3/Cy5 (DIF3/no treatment)
>> Slide18 Cy5/Cy3 (DIF3/no treatment)
>>
>> I'd obviously like to compare across the different treatments DIF1,2
>> and 3
-- 
-isaac mehl
gene expression lab (gele)
salk institute
10010 n. torrey pines rd.
la jolla ca. 92037
http://genex.salk.edu